Relax 4.1.2 - Revision history

Bugman: Added relax 4.1.3 as the next release in the infobox.

2019-06-14T09:43:07Z

Added relax 4.1.3 as the next release in the infobox.

Bugman: Added some keywords.

2019-04-26T14:17:55Z

Added some keywords.

Bugman: /* Links */ Corrected the mailing list message link.

2019-04-26T14:13:13Z

Links: Corrected the mailing list message link.

Bugman: /* Description */ Wrote a description for the release.

2019-04-26T14:01:45Z

Description: Wrote a description for the release.

Bugman: Conversion of the direct links.

2019-04-26T13:49:30Z

Conversion of the direct links.

Bugman: Added `tags for better formatting.`


2019-04-26T12:56:34Z
Added <code> tags for better formatting.

				
				
				
				
				
				← Older revision
				Revision as of 12:56, 26 April 2019
				
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  * Release checklist document: Updated the text to better match the new release process.   * Release checklist document: Updated the text to better match the new release process.
  * HTML manual: CSS fix for newer LaTeX2HTML versions.  The text width in the HTML appears to now be fixed to a maximum width matching the text dimensions in the PDF.  This looks bad together with the wider images and code snippets.   * HTML manual: CSS fix for newer LaTeX2HTML versions.  The text width in the HTML appears to now be fixed to a maximum width matching the text dimensions in the PDF.  This looks bad together with the wider images and code snippets.
− * System tests: Added two tests to catch [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the failure to catch the '#' character when setting the molecule name].  The tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_arg Structure.test_bug_12_hash_in_mol_name_via_arg] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_file Structure.test_bug_12_hash_in_mol_name_via_file].  These cover the two ways a '#' character can enter a molecule name - via the file name or via the set_mol_name argument.  Both the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] and [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions are checked. + * System tests: Added two tests to catch [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the failure to catch the '#' character when setting the molecule name].  The tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_arg Structure.test_bug_12_hash_in_mol_name_via_arg] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_file Structure.test_bug_12_hash_in_mol_name_via_file].  These cover the two ways a <code>#</code> character can enter a molecule name - via the file name or via the set_mol_name argument.  Both the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] and [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions are checked.
  * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T1_read_fail Bruker.test_bug_13_T1_read_fail] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T2_read_fail Bruker.test_bug_13_T2_read_fail] and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13].   * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T1_read_fail Bruker.test_bug_13_T1_read_fail] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T2_read_fail Bruker.test_bug_13_T2_read_fail] and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13].
  * User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read] text.   * User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read] text.
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  * Test suite: The keyboard interrupt terminates the test suite once again.   * Test suite: The keyboard interrupt terminates the test suite once again.
  * FSF Copyright Validation script: The return status now starts at 0 to allow for early returns.   * FSF Copyright Validation script: The return status now starts at 0 to allow for early returns.
− * FSF Copyright Validation script: Support for saving and reading the committer information.  This allows the committer information (file name, committer name, and copyright years) from older repositories to be saved and later read into the script.  In this case, the old Subversion history has been read and the committer information placed into the fsfcv.svn_committer_info.bz2 file (in the devel_scripts/ directory).  This compressed file is now specified in the fsfcv.conf.py configuration file.  The result is that the fsfcv script can be run on the relax git repository without requiring a checkout of the old SVN repository. + * FSF Copyright Validation script: Support for saving and reading the committer information.  This allows the committer information (file name, committer name, and copyright years) from older repositories to be saved and later read into the script.  In this case, the old Subversion history has been read and the committer information placed into the <code>fsfcv.svn_committer_info.bz2</code> file (in the <code>devel_scripts/</code> directory).  This compressed file is now specified in the <code>fsfcv.conf.py</code> configuration file.  The result is that the <code>fsfcv</code> script can be run on the relax git repository without requiring a checkout of the old SVN repository.
  * Travis CI config: Improvements to the comments and spacing.   * Travis CI config: Improvements to the comments and spacing.
− * API manual: Scons compilation via epydoc now fails if a warning or error is found.  This manually parses the epydoc output to skip the unavoidable wxPython warnings.  Any error or warning will now cause an error to be raised.  This results in a non-zero return code from scons to allow the api_manual_html target to be checked in scripts. + * API manual: Scons compilation via epydoc now fails if a warning or error is found.  This manually parses the epydoc output to skip the unavoidable wxPython warnings.  Any error or warning will now cause an error to be raised.  This results in a non-zero return code from scons to allow the <code>api_manual_html</code> target to be checked in scripts.
  * Travis CI config: Named all of the jobs.   * Travis CI config: Named all of the jobs.
  * Travis CI config: General clean up and execution of the software verification tests.   * Travis CI config: General clean up and execution of the software verification tests.
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  * Travis CI config: Alphabetical ordering of environmental variables and required Python packages.   * Travis CI config: Alphabetical ordering of environmental variables and required Python packages.
  * Travis CI config: Creation of an API documentation build job.   * Travis CI config: Creation of an API documentation build job.
− * Travis CI config: Fix for the Mac OS X build.  This job passes, but the test suite fails with the following traceback message when trying to import matplotlib: "ImportError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.". The fix is simply to create $HOME/.matplotlib/matplotlibrc with the contents 'backend: TkAgg'. + * Travis CI config: Fix for the Mac OS X build.  This job passes, but the test suite fails with the following traceback message when trying to import matplotlib: "ImportError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.". The fix is simply to create <code>$HOME/.matplotlib/matplotlibrc</code> with the contents <code>backend: TkAgg</code>.
− * API manual: Greater filtering of the file list passed to epydoc.  Now only relax modules ending in *.py are processed.  That means that all base directory scripts, including 'sconstruct', are excluded from the API documentation. + * API manual: Greater filtering of the file list passed to epydoc.  Now only relax modules ending in <code>*.py</code> are processed.  That means that all base directory scripts, including <code>sconstruct</code>, are excluded from the API documentation.
  * API manual: More reliable parsing of the epydoc output to detect non-wxPython issues.   * API manual: More reliable parsing of the epydoc output to detect non-wxPython issues.
  * FSF Copyright Validation configuration: Improvements to the repository configuration section.  The different configurations can now be chosen via a variable, rather than requiring code to be uncommented.   * FSF Copyright Validation configuration: Improvements to the repository configuration section.  The different configurations can now be chosen via a variable, rather than requiring code to be uncommented.
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  <section begin=bugfixes/>   <section begin=bugfixes/>
− * relax GUI: wxPython-Phoenix 4.x fix to allow relax to start again.  In the later wxPython versions, relax would not be able to start either the GUI or any of the test suite due to a new error "wx._core.PyNoAppError: The wx.App object must be created first!".  This was not present in wxPython-Phoenix 3.  The [http://www.nmr-relax.com/api/4.1/gui.icons.Relax_icons-class.html Relax_icons class] (a wx.IconBundle derived class) is no longer instantiated on import. + * relax GUI: wxPython-Phoenix 4.x fix to allow relax to start again.  In the later wxPython versions, relax would not be able to start either the GUI or any of the test suite due to a new error "wx._core.PyNoAppError: The wx.App object must be created first!".  This was not present in wxPython-Phoenix 3.  The [http://www.nmr-relax.com/api/4.1/gui.icons.Relax_icons-class.html Relax_icons class] (a <code>wx.IconBundle</code> derived class) is no longer instantiated on import.
− * Structure loading: Fix for [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the acceptance of the invalid '#' character in molecule names].  A simple check has not been added to the [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object.Internal-class.html#load_pdb load_pdb()] and [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object.Internal-class.html#load_xyz load_xyz()] functions of the [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object-module.html internal structural object in lib.structure.internal.object].  This ensures that the '#' character can never be set as the molecule name, independently if it was taken from a file name or set via the set_mol_name arguments of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] or [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions. + * Structure loading: Fix for [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the acceptance of the invalid '#' character in molecule names].  A simple check has not been added to the [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object.Internal-class.html#load_pdb load_pdb()] and [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object.Internal-class.html#load_xyz load_xyz()] functions of the [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object-module.html internal structural object in lib.structure.internal.object].  This ensures that the <code>#</code> character can never be set as the molecule name, independently if it was taken from a file name or set via the <code>set_mol_name</code> arguments of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] or [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions.
  * Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions.  This fixes [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13, the failure of reading newer Bruker DC files].  The backend has been resigned so that the relax library produces a [http://www.nmr-relax.com/api/4.1/lib.software.bruker_dc.DCObject-class.html complex Python object representation of the Bruker DC results file].  This object now stores all of the data present within the Bruker DC file.  The design is more flexible as precise column ordering no longer matters.   * Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions.  This fixes [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13, the failure of reading newer Bruker DC files].  The backend has been resigned so that the relax library produces a [http://www.nmr-relax.com/api/4.1/lib.software.bruker_dc.DCObject-class.html complex Python object representation of the Bruker DC results file].  This object now stores all of the data present within the Bruker DC file.  The design is more flexible as precise column ordering no longer matters.
  * Fix for [https://sourceforge.net/p/nmr-relax/tickets/14/ bug #14, the freezing of user functions in the GUI].  The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor.  These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter.  Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in [[relax 4.1.0]].  These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor.   * Fix for [https://sourceforge.net/p/nmr-relax/tickets/14/ bug #14, the freezing of user functions in the GUI].  The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor.  These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter.  Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in [[relax 4.1.0]].  These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor.
− * GUI bug fix: Avoidance of the numpy depreciation of '== None'.  This deprecation causes the GUI to fail with recent numpy versions. + * GUI bug fix: Avoidance of the numpy depreciation of <code>== None</code>.  This deprecation causes the GUI to fail with recent numpy versions.
− * Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification.  These are now only used with copy.deepcopy().  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'.  The system tests add 'r1' and then the unit tests subsequently fail.  This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax. + * Relaxation dispersion: Protection of all of the <code>MODEL_PARAMS_*</code> variables from modification.  These are now only used with <code>copy.deepcopy()</code>.  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of <code>'r1'</code>.  The system tests add <code>'r1'</code> and then the unit tests subsequently fail.  This would also be an issue if an experiment without the <code>'r1'</code> parameter is analysed after one with that parameter, without restarting relax.
− * Relaxation dispersion bug fix: The 'r1' parameter was missing from the nested parameter algorithm.  This is the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html#nesting_param nesting_param() function] of the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.model module].  The 'r1' parameter must be treated differently from the other model parameters, just as the 'r2*' parameters are. + * Relaxation dispersion bug fix: The <code>'r1'</code> parameter was missing from the nested parameter algorithm.  This is the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html#nesting_param nesting_param() function] of the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.model module].  The <code>'r1'</code> parameter must be treated differently from the other model parameters, just as the <code>'r2*'</code> parameters are.
− * Dispersion auto-analysis: Bug fix for the plotting of the {{:R1}} parameter.  The plotting relied on the insertion of the 'r1' parameter into the read only MODEL_PARAMS_* variables of [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html lib.dispersion.variables].  Now the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model.Model_class-class.html Model_class class] from [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.model] is being used to dynamically determine the parameters of the model. + * Dispersion auto-analysis: Bug fix for the plotting of the {{:R1}} parameter.  The plotting relied on the insertion of the <code>'r1'</code> parameter into the read only <code>MODEL_PARAMS_*</code> variables of [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html lib.dispersion.variables].  Now the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model.Model_class-class.html Model_class class] from [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.model] is being used to dynamically determine the parameters of the model.
  <section end=bugfixes/>   <section end=bugfixes/>



Bugman: Extensive links to the API documentation.
2019-04-26T12:50:42Z
Extensive links to the API documentation.

				
				
				
				
				
				← Older revision
				Revision as of 12:50, 26 April 2019
				
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  * Release checklist document: Updated the text to better match the new release process.   * Release checklist document: Updated the text to better match the new release process.
  * HTML manual: CSS fix for newer LaTeX2HTML versions.  The text width in the HTML appears to now be fixed to a maximum width matching the text dimensions in the PDF.  This looks bad together with the wider images and code snippets.   * HTML manual: CSS fix for newer LaTeX2HTML versions.  The text width in the HTML appears to now be fixed to a maximum width matching the text dimensions in the PDF.  This looks bad together with the wider images and code snippets.
− * System tests: Added two tests to catch [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the failure to catch the '#' character when setting the molecule name].  The tests are Structure.test_bug_12_hash_in_mol_name_via_arg and Structure.test_bug_12_hash_in_mol_name_via_file.  These cover the two ways a '#' character can enter a molecule name - via the file name or via the set_mol_name argument.  Both the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] and [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions are checked. + * System tests: Added two tests to catch [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the failure to catch the '#' character when setting the molecule name].  The tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_arg Structure.test_bug_12_hash_in_mol_name_via_arg] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.structure.Structure-class.html#test_bug_12_hash_in_mol_name_via_file Structure.test_bug_12_hash_in_mol_name_via_file].  These cover the two ways a '#' character can enter a molecule name - via the file name or via the set_mol_name argument.  Both the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] and [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions are checked.
− * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are Bruker.test_bug_13_T1_read_fail and Bruker.test_bug_13_T2_read_fail and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13]. + * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T1_read_fail Bruker.test_bug_13_T1_read_fail] and [http://www.nmr-relax.com/api/4.1/test_suite.system_tests.bruker.Bruker-class.html#test_bug_13_T2_read_fail Bruker.test_bug_13_T2_read_fail] and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13].
  * User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read] text.   * User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read] text.
  * User manual: Clean up of the bibliography entry titles.  Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, {{:R1rho}}, {{:R2}}, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex.   * User manual: Clean up of the bibliography entry titles.  Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, {{:R1rho}}, {{:R2}}, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex.
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  <section begin=bugfixes/>   <section begin=bugfixes/>
− * relax GUI: wxPython-Phoenix 4.x fix to allow relax to start again.  In the later wxPython versions, relax would not be able to start either the GUI or any of the test suite due to a new error "wx._core.PyNoAppError: The wx.App object must be created first!".  This was not present in wxPython-Phoenix 3.  The Relax_icons class (a wx.IconBundle derived class) is no longer instantiated on import. + * relax GUI: wxPython-Phoenix 4.x fix to allow relax to start again.  In the later wxPython versions, relax would not be able to start either the GUI or any of the test suite due to a new error "wx._core.PyNoAppError: The wx.App object must be created first!".  This was not present in wxPython-Phoenix 3.  The [http://www.nmr-relax.com/api/4.1/gui.icons.Relax_icons-class.html Relax_icons class] (a wx.IconBundle derived class) is no longer instantiated on import.
− * Structure loading: Fix for [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the acceptance of the invalid '#' character in molecule names].  A simple check has not been added to the load_pdb() and load_xyz() functions of the internal structural object in lib.structure.internal.object.  This ensures that the '#' character can never be set as the molecule name, independently if it was taken from a file name or set via the set_mol_name arguments of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] or [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions. + * Structure loading: Fix for [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the acceptance of the invalid '#' character in molecule names].  A simple check has not been added to the [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object.Internal-class.html#load_pdb load_pdb()] and [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object.Internal-class.html#load_xyz load_xyz()] functions of the [http://www.nmr-relax.com/api/4.1/lib.structure.internal.object-module.html internal structural object in lib.structure.internal.object].  This ensures that the '#' character can never be set as the molecule name, independently if it was taken from a file name or set via the set_mol_name arguments of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] or [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions.
− * Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions.  This fixes [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13, the failure of reading newer Bruker DC files].  The backend has been resigned so that the relax library produces a complex Python object representation of the Bruker DC results file.  This object now stores all of the data present within the Bruker DC file.  The design is more flexible as precise column ordering no longer matters. + * Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions.  This fixes [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13, the failure of reading newer Bruker DC files].  The backend has been resigned so that the relax library produces a [http://www.nmr-relax.com/api/4.1/lib.software.bruker_dc.DCObject-class.html complex Python object representation of the Bruker DC results file].  This object now stores all of the data present within the Bruker DC file.  The design is more flexible as precise column ordering no longer matters.
  * Fix for [https://sourceforge.net/p/nmr-relax/tickets/14/ bug #14, the freezing of user functions in the GUI].  The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor.  These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter.  Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in [[relax 4.1.0]].  These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor.   * Fix for [https://sourceforge.net/p/nmr-relax/tickets/14/ bug #14, the freezing of user functions in the GUI].  The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor.  These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter.  Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in [[relax 4.1.0]].  These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor.
  * GUI bug fix: Avoidance of the numpy depreciation of '== None'.  This deprecation causes the GUI to fail with recent numpy versions.   * GUI bug fix: Avoidance of the numpy depreciation of '== None'.  This deprecation causes the GUI to fail with recent numpy versions.
  * Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification.  These are now only used with copy.deepcopy().  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'.  The system tests add 'r1' and then the unit tests subsequently fail.  This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax.   * Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification.  These are now only used with copy.deepcopy().  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'.  The system tests add 'r1' and then the unit tests subsequently fail.  This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax.
− * Relaxation dispersion bug fix: The 'r1' parameter was missing from the nested parameter algorithm.  This is the nesting_param() function of the specific_analyses.relax_disp.model module.  The 'r1' parameter must be treated differently from the other model parameters, just as the 'r2*' parameters are. + * Relaxation dispersion bug fix: The 'r1' parameter was missing from the nested parameter algorithm.  This is the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html#nesting_param nesting_param() function] of the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.model module].  The 'r1' parameter must be treated differently from the other model parameters, just as the 'r2*' parameters are.
− * Dispersion auto-analysis: Bug fix for the plotting of the {{:R1}} parameter.  The plotting relied on the insertion of the 'r1' parameter into the read only MODEL_PARAMS_* variables of lib.dispersion.variables.  Now the Model_class class from specific_analyses.relax_disp.models is being used to dynamically determine the parameters of the model. + * Dispersion auto-analysis: Bug fix for the plotting of the {{:R1}} parameter.  The plotting relied on the insertion of the 'r1' parameter into the read only MODEL_PARAMS_* variables of [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html lib.dispersion.variables].  Now the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model.Model_class-class.html Model_class class] from [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model-module.html specific_analyses.relax_disp.model] is being used to dynamically determine the parameters of the model.
  <section end=bugfixes/>   <section end=bugfixes/>
    



Bugman: Converted all parameters to use parameter templates.
2019-04-26T12:37:33Z
Converted all parameters to use parameter templates.

				
				
				
				
				
				← Older revision
				Revision as of 12:37, 26 April 2019
				
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  * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are Bruker.test_bug_13_T1_read_fail and Bruker.test_bug_13_T2_read_fail and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13].   * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are Bruker.test_bug_13_T1_read_fail and Bruker.test_bug_13_T2_read_fail and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13].
  * User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read] text.   * User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read] text.
− * User manual: Clean up of the bibliography entry titles.  Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, R1rho, R2, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex. + * User manual: Clean up of the bibliography entry titles.  Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, {{:R1rho}}, {{:R2}}, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex.
  * User manual: Standardisation of the frame order indexing.   * User manual: Standardisation of the frame order indexing.
  * User manual: Standardisation of the relaxation dispersion indexing.   * User manual: Standardisation of the relaxation dispersion indexing.
Line 88:
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  * Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification.  These are now only used with copy.deepcopy().  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'.  The system tests add 'r1' and then the unit tests subsequently fail.  This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax.   * Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification.  These are now only used with copy.deepcopy().  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'.  The system tests add 'r1' and then the unit tests subsequently fail.  This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax.
  * Relaxation dispersion bug fix: The 'r1' parameter was missing from the nested parameter algorithm.  This is the nesting_param() function of the specific_analyses.relax_disp.model module.  The 'r1' parameter must be treated differently from the other model parameters, just as the 'r2*' parameters are.   * Relaxation dispersion bug fix: The 'r1' parameter was missing from the nested parameter algorithm.  This is the nesting_param() function of the specific_analyses.relax_disp.model module.  The 'r1' parameter must be treated differently from the other model parameters, just as the 'r2*' parameters are.
− * Dispersion auto-analysis: Bug fix for the plotting of the R1 parameter.  The plotting relied on the insertion of the 'r1' parameter into the read only MODEL_PARAMS_* variables of lib.dispersion.variables.  Now the Model_class class from specific_analyses.relax_disp.models is being used to dynamically determine the parameters of the model. + * Dispersion auto-analysis: Bug fix for the plotting of the {{:R1}} parameter.  The plotting relied on the insertion of the 'r1' parameter into the read only MODEL_PARAMS_* variables of lib.dispersion.variables.  Now the Model_class class from specific_analyses.relax_disp.models is being used to dynamically determine the parameters of the model.
  <section end=bugfixes/>   <section end=bugfixes/>
    



Bugman: One more user function link.
2019-04-26T12:34:26Z
One more user function link.

				
				
				
				
				
				← Older revision
				Revision as of 12:34, 26 April 2019
				
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  * System tests: Added two tests to catch [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the failure to catch the '#' character when setting the molecule name].  The tests are Structure.test_bug_12_hash_in_mol_name_via_arg and Structure.test_bug_12_hash_in_mol_name_via_file.  These cover the two ways a '#' character can enter a molecule name - via the file name or via the set_mol_name argument.  Both the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] and [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions are checked.   * System tests: Added two tests to catch [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the failure to catch the '#' character when setting the molecule name].  The tests are Structure.test_bug_12_hash_in_mol_name_via_arg and Structure.test_bug_12_hash_in_mol_name_via_file.  These cover the two ways a '#' character can enter a molecule name - via the file name or via the set_mol_name argument.  Both the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] and [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions are checked.
  * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are Bruker.test_bug_13_T1_read_fail and Bruker.test_bug_13_T2_read_fail and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13].   * Test suite: 2 new system tests to catch the failure of reading newer Bruker DC files.  The system tests are Bruker.test_bug_13_T1_read_fail and Bruker.test_bug_13_T2_read_fail and these catch [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13].
− * User function definitions: Clarifications for the bruker.read text. + * User function definitions: Clarifications for the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read] text.
  * User manual: Clean up of the bibliography entry titles.  Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, R1rho, R2, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex.   * User manual: Clean up of the bibliography entry titles.  Species names are properly italicised with genus names capitalised, nuclear isotopes are superscripted, R1rho, R2, etc. are properly subscripted, the Perrin articles are translated into English, symbols are now symbols, and unnecessary capitalisation has been removed from the bibtex.
  * User manual: Standardisation of the frame order indexing.   * User manual: Standardisation of the frame order indexing.



Bugman: Internal links for all relax versions.
2019-04-26T12:32:53Z
Internal links for all relax versions.

				
				
				
				
				
				← Older revision
				Revision as of 12:32, 26 April 2019
				
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  * Structure loading: Fix for [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the acceptance of the invalid '#' character in molecule names].  A simple check has not been added to the load_pdb() and load_xyz() functions of the internal structural object in lib.structure.internal.object.  This ensures that the '#' character can never be set as the molecule name, independently if it was taken from a file name or set via the set_mol_name arguments of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] or [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions.   * Structure loading: Fix for [https://sourceforge.net/p/nmr-relax/tickets/12/ bug #12, the acceptance of the invalid '#' character in molecule names].  A simple check has not been added to the load_pdb() and load_xyz() functions of the internal structural object in lib.structure.internal.object.  This ensures that the '#' character can never be set as the molecule name, independently if it was taken from a file name or set via the set_mol_name arguments of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] or [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz] user functions.
  * Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions.  This fixes [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13, the failure of reading newer Bruker DC files].  The backend has been resigned so that the relax library produces a complex Python object representation of the Bruker DC results file.  This object now stores all of the data present within the Bruker DC file.  The design is more flexible as precise column ordering no longer matters.   * Bruker DC: Complete redesign of the backend to support reading newer (or older) file versions.  This fixes [https://sourceforge.net/p/nmr-relax/tickets/13/ bug #13, the failure of reading newer Bruker DC files].  The backend has been resigned so that the relax library produces a complex Python object representation of the Bruker DC results file.  This object now stores all of the data present within the Bruker DC file.  The design is more flexible as precise column ordering no longer matters.
− * Fix for [https://sourceforge.net/p/nmr-relax/tickets/14/ bug #14, the freezing of user functions in the GUI].  The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor.  These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter.  Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in relax 4.1.0.  These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor. + * Fix for [https://sourceforge.net/p/nmr-relax/tickets/14/ bug #14, the freezing of user functions in the GUI].  The user functions freeze if an error occurs that is not a RelaxError, with the mouse pointer stuck on the busy cursor.  These non-RelaxErrors are now caught and manually dealt with by the GUI interpreter.  Like all GUI freezing bugs, this was introduced with the huge GUI speed up prior in [[relax 4.1.0]].  These also only to appear to be a freeze, but it is actually the failure to update and show the relax controller combined with not turning off the busy mouse cursor.
  * GUI bug fix: Avoidance of the numpy depreciation of '== None'.  This deprecation causes the GUI to fail with recent numpy versions.   * GUI bug fix: Avoidance of the numpy depreciation of '== None'.  This deprecation causes the GUI to fail with recent numpy versions.
  * Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification.  These are now only used with copy.deepcopy().  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'.  The system tests add 'r1' and then the unit tests subsequently fail.  This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax.   * Relaxation dispersion: Protection of all of the MODEL_PARAMS_* variables from modification.  These are now only used with copy.deepcopy().  This removes a number of bugs in which the lists, which should be read-only, are permanently modified by the addition of 'r1'.  The system tests add 'r1' and then the unit tests subsequently fail.  This would also be an issue if an experiment without the 'r1' parameter is analysed after one with that parameter, without restarting relax.

@@ Line 4: / Line 4: @@
 | version  = 4.1.2
 | prev     = 4.1.1
 | keywords = Frame order, GUI, manual
 | type     = Minor feature and bugfix

@@ Line 4: / Line 4: @@
 | version  = 4.1.2
 | prev     = 4.1.1
-| keywords =
+| keywords = Frame order, GUI, manual
 | type     = Minor feature and bugfix
 | date     = 25 April 2019

@@ Line 100: / Line 100: @@
 * [http://wiki.nmr-relax.com/Relax_4.1.2 Official release notes on the relax wiki].
-* [https://sourceforge.net/p/nmr-relax/mailman/message/36607157/ Mailing list message].
+* [https://sourceforge.net/p/nmr-relax/mailman/message/36650583/ Mailing list message].
 * [https://www.mail-archive.com/nmr-relax-announce@lists.sourceforge.net/msg00003.html The Mail Archive].

← Older revision		Revision as of 14:01, 26 April 2019
Line 13:		Line 13:

	<section begin=description/>		<section begin=description/>
		+	This is a minor feature and bugfix release. It includes tooltip improvements in the GUI for the user function windows and wizards, the addition of the newly published [https://doi.org/10.1017/S0033583519000015 primary reference for the frame order analysis], and improved formatting for the bibliography and index of the relax manual.
		+
		+	There have also been improvements for the [https://travis-ci.com/nmr-relax/relax automated testing of relax by Travis CI]. This includes the naming of the build jobs, the execution of the software verification tests, the installation of wxPython to enable GUI testing and the running of the whole test suite, the reordering of the system tests back before the unit tests to avoid hiding some nasty relaxation dispersion bugs, a fix for matplotlib on Mac OS X so that the tests will finally run on this OS, a new build job for the API documentation, and a new build job for the Free Software Foundation copyright validation script.
	<section end=description/>		<section end=description/>

@@ Line 49: / Line 49: @@
 * User manual: Standardisation of the frame order indexing.
 * User manual: Standardisation of the relaxation dispersion indexing.
-* Travis CI config: Attempt at installing wxPython for Ubuntu and Python 2.7.  This would allow for the whole test suite to be run on Travis CI on at least one OS.  The instructions come from the stackoverflow response by dthor at https://stackoverflow.com/questions/29290011/using-travis-ci-with-wxpython-tests.
+* Travis CI config: Attempt at installing wxPython for Ubuntu and Python 2.7.  This would allow for the whole test suite to be run on Travis CI on at least one OS.  The instructions come from the [https://stackoverflow.com/questions/29290011/using-travis-ci-with-wxpython-tests stackoverflow response by dthor].
 * FSF Copyright Validation script: The script now returns an exit status.
 * Travis CI config: Avoid updating Conda.  This seems to cause a breakage in installing matplotlib.

Relax 4.1.2 - Revision history

Bugman: Added relax 4.1.3 as the next release in the infobox.

Bugman: Added some keywords.

Bugman: /* Links */ Corrected the mailing list message link.

Bugman: /* Description */ Wrote a description for the release.

Bugman: Conversion of the direct links.

Bugman: Added tags for better formatting.

Bugman: Extensive links to the API documentation.

Bugman: Converted all parameters to use parameter templates.

Bugman: One more user function link.

Bugman: Internal links for all relax versions.

Bugman: Added `tags for better formatting.`